For future reference, Doxygen can easily be configured to ignore certain macros:

# ======================================
# Allow us to define our own list of
# macros to expand during preprocessing
# ======================================
ENABLE_PREPROCESSING=YESMACRO_EXPANSION=YESEXPAND_ONLY_PREDEF=YES# --------------------------------------
# A list of all of the macros to expand,
# in the form <macro>=<expansion>.
# --------------------------------------
PREDEFINED=__attribute__(x)=PREDEFINED+=_Pragma(x)=